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Software Tools for Computational Molecular Biology

Practical Course: "Software Tools for Computational Molecular Biology", WS2003

 

 
General Subject: Bioinformatik, Practical informatics
Tutors:
 PD Dr. Olaf Delgado-Friedrichs, Tobias Dezulian und Christian Rausch
Time:
Wednesday 13:15-17:00
Amount: 4 SWS, allowable: 2 SWS
Location: Poolroom Sand 6/7
Home page: http://www-ab.informatik.uni-tuebingen.de/teaching/ws03/tool/welcome.html
Description:
In this tutorial we want to look at several software tools that are widely used at the moment.
E.g.: Programs for sequence comarison (pairwise and multiple alignments, e.g. ClustalW, T-Coffee), programs for phylogenetic reconstruction (e.g. Phylip, Paup, SplitsTree), database search (e.g. BLAST, HMMer), vizualisation (e.g. CGViz), genefinding (e.g. genscan) and others.
Requirements for admission:
completed Vordiplom Bioinformatik, the lectures "Algorithms in Bioinformatics I and II" are recommended.
Remark: The course has started, no further participants may be admitted.

 

 

Working material:

Session 22 Oct 2003: Sequence analysis with EMBOSS

pUC19.seq: sequence of a cloning vector in gcg format
Exercise: A study of a human protein

 

Listing of sessions with protocols:

 

 

  1. Sequence analysis with EMBOSS and study of a human protein (Protocol by Kristoffer Forslund)

  2. Introduction to phylogeny and the program package PAUP for phylogenetic analysis (Protocol by Serhat Saydam)

  3. Repeat detection with suffix trees using MUMmer, application to detection of miRNAs in Arabidopsis (Protocol by Holger Plattfaut)

  4. miRNAs, continued (Protocol by Michael Remmert)

  5. Hidden Markov Models and HMMer (Protocol by Helge Florin)

  6. Geneprediction using Genscan (Protocol by Christian Mayer)

  7. Introduction to Blast, theoretical and practical (Protocol by Mathias Ganter)

  8. Blast and visualization of genetic data with CGViz (Protocol continued by Mathias Ganter)

  9. Support Vector Machines (Protocol by Andreas Biegert)

 

 

All protocols in one pdf for download

 

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